Package org.biopax.paxtools.pattern.miner

Class RelatedGenesOfInteractionsMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.RelatedGenesOfInteractionsMiner

All Implemented Interfaces:

Miner

public class RelatedGenesOfInteractionsMiner
extends MinerAdapter

Miner for the related genes (participant or controller) of interactions.

Author:

Ozgun Babur

Field Summary

Fields inherited from class org.biopax.paxtools.pattern.miner.MinerAdapter

blacklist, description, idFetcher, idMap, name

Constructor Summary

Constructors

Constructor	Description
RelatedGenesOfInteractionsMiner()	Constructor that sets name and description.

Method Summary

Modifier and Type	Method	Description
Pattern	constructPattern()	Constructs the pattern.
void	writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out)	Writes the IDs of interaction, then gene symbols of related proteins in a line.

Methods inherited from class org.biopax.paxtools.pattern.miner.MinerAdapter

concat, createSIFInteraction, fetchIDs, getCellularLocations, getChain, getCompoundName, getDeltaCompartments, getDeltaModifications, getDescription, getGeneSymbol, getGeneSymbol, getHeader, getIdentifiers, getIdMap, getMediatorLabels, getModifications, getModifications, getModificationTerm, getName, getPattern, getPositionInString, getPositionStart, getRelationType, getSourcePELabels, getTargetPELabels, getUniprotNameForHuman, getUniprotNameForHuman, getValue, isInhibition, labeledInactive, removeCommon, setBlacklist, setDescription, setIDFetcher, setIdMap, setName, sign, sign, toString, toStringSet, writeResultAsSIF, writeResultDetailed, writeSIFsUsingSIFFramework

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

RelatedGenesOfInteractionsMiner

public RelatedGenesOfInteractionsMiner()

Constructor that sets name and description.

Method Details

constructPattern

public Pattern constructPattern()

Constructs the pattern.

Specified by:

constructPattern in class MinerAdapter

Returns:

pattern

writeResult

public void writeResult(Map<BioPAXElement,List<Match>> matches,
 OutputStream out)
                 throws IOException

Writes the IDs of interaction, then gene symbols of related proteins in a line.

Parameters:

matches - pattern search result

out - output stream

Throws:

IOException - when there's a problem writing to the output stream